We sought to investigate whether the magnitude of differences in cycling critical power between normoxia and hypoxia (∆CP) is associated with fitness level or haematological status in highly trained endurance athletes. Thirty-three triathletes and longtrack speed skaters (11 females) completed two 3-minute CP cycling tests: one in normoxia (F_iO₂ = 20.8%) and the other in normobaric hypoxia (F_iO₂ = 14.2%). This cross-sectional study analysed ∆CP regarding performance, physiological, and haematological indices using correlation and regression analyses. Significant correlations were found between ∆CP and baseline CP in normoxia (r = -0.366, p = 0.047), V̇ O_2max (r = -0.437, p = 0.018), and MCH (r = 0.487, p = 0.012). Only a few significant associations were found between the indices obtained from venous blood sampling and ∆CP, different for females and males. In females, ∆CP was correlated with Hbmass (r = -0.761, p = 0.017), erythrocyte volume (r = -0.783, p = 0.013), plasma volume (r = -0.745, p = 0.021), and blood volume (r = -0.870, p = 0.002), all established with the CO rebreathing method. The best-performing regression model (R² = 0.501, RMSE = 0.033, p = 0.002, Cohen’s F² = 1.004) included MCH, V̇ O_2max, and Hb_mass. A higher fitness level is associated with a greater CP decrease in hypoxia among the homogeneous cohort of highly trained endurance athletes. Haematological status plays a more prominent role in females, and the CO rebreathing method should be considered a preferred approach for assessing haematological status in highly trained athletes.